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Re: [ccp4bb]: High and low B-factors
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Ralf Bienert wrote:
>
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> Hello everybody!
>
> I solved a SAD structure to 1.8 A of a Se-Met protein and refine it with
> refmac5.
> However, I observed negative difference density around my Se-sites,
> together with high B-factors of this atoms. I think this is due to
> radiation damage. So far it is interpretable.
> But why do I have so low B-values for my CE atoms, even lower than the
> B-value of the other atoms of Se-Met.
> My question now is how to interprete this observation and how to deal with
> it. I just set the occupancy of both atoms to lower (same) values to get
> rid of the negative difference density, but is this the right way???? Of
> course, the B-value decresed, as well of CE.
>
> To get an idea I list my "worst" data (occupancy=1, B-value):
>
> N MSE 1.00 45.98 N
> CA MSE 1.00 45.15 C
> CB MSE 1.00 43.74 C
> CG MSE 1.00 44.29 C
> SE MSE 1.00 49.38 SE
> CE MSE 1.00 9.79 C
> C MSE 1.00 43.49 C
> O MSE 1.00 44.28 O
>
> N MSE 1.00 25.08 N
> CA MSE 1.00 25.90 C
> CB MSE 1.00 25.00 C
> CG MSE 1.00 29.97 C
> SE MSE 1.00 35.56 SE
> CE MSE 1.00 19.57 C
> C MSE 1.00 24.97 C
> O MSE 1.00 23.98 O
>
> Thanks in advance.
> Ralf
You dont say the wave length but the default formfactor for SE will not
have any f' modification, so the B factor is trying to correct for that
I guess..
Why your CE B factor is so low is so low I cant think - Eleanor